diff PanExplorer_workflow/Perl/ConvertPanarooMatrix.pl @ 1:032f6b3806a3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PanExplorer_workflow/Perl/ConvertPanarooMatrix.pl	Thu May 30 11:16:08 2024 +0000
@@ -0,0 +1,106 @@
+#!/usr/bin/perl
+
+use strict;
+
+my $indir = $ARGV[0];
+my $matrix = $ARGV[1];
+my $out = $ARGV[2];
+my $strain_names = $ARGV[3];
+
+my %strains_of_gb;
+open(F,$strain_names);
+while(<F>){
+	my $line = $_;
+	$line =~s/\n//g;$line =~s/\r//g;
+	my ($gb,$strain) = split(/\t/,$line);
+	$strains_of_gb{$gb} = $strain;
+}
+close(F);
+
+
+my %corr;
+open(D,"ls $indir/*rmdup.gff |");
+while(<D>){
+	my $file = $_;
+	open(F,"$file");
+        while(<F>){
+                my @infos = split(/\t/,$_);
+                if ($infos[2] eq 'CDS' && /ID=([^;]*);.*protein_id=([^;]*);/){
+                        my $id = $1;
+                        my $protid = $2;
+                        $corr{$id} = $protid;
+                }
+        }
+        close(F);
+}
+close(D);
+
+my $cl_num = 0;
+my $nb_strains = 1;
+open(O,">$out");
+open(U,">$out.upsetr.txt");
+open(M,">$out.accessory_01matrix.txt");
+open(F,$matrix);
+my $firstline = <F>;
+$firstline =~s/\n//g;$firstline =~s/\r//g;
+my @infos = split(/,/,$firstline);
+print O "ClutserID";
+print U "ClutserID";
+print M "Gene";
+for (my $j=14; $j <= $#infos; $j++){
+        my $gbfile = $infos[$j];
+        $gbfile =~s/\"//g;
+        $gbfile =~s/\.gb\.filt//g;
+	$gbfile =~s/\.gb\.rmdup//g;
+	
+        my $strain = $strains_of_gb{$gbfile};
+        print O "\t".$strain;
+        print U "\t".$strain;
+        print M "\t".$strain;
+        $nb_strains++;
+}
+print O "\n";
+print U "\n";
+print M "\n";
+while(<F>){
+        $cl_num++;
+        my $line = $_;
+        $line =~s/\n//g;$line =~s/\r//g;
+        my @infos = split(/,/,$line);
+        print O $cl_num;
+        print U $cl_num;
+        my $concat_accessory = "";
+        for (my $i = 14; $i <= $#infos; $i++){
+                my $val = $infos[$i];
+                $val =~s/\"//g;
+                if ($val =~/\w+/){
+                        print U "\t1";
+                        $concat_accessory .= "\t1";
+                }
+                else{
+                        print U "\t0";
+                        $concat_accessory .= "\t0";
+                }
+                my @genes = split(/;/,$val);
+                my $concat = "";
+                foreach my $gene(@genes){
+                        my $prot_id = $corr{$gene};
+			if (!$prot_id){$prot_id = $gene;}
+                        $concat .= "$prot_id,"
+                }
+                chop($concat);
+                if (scalar @genes == 0){
+                        $concat = "-";
+                }
+                print O "\t".$concat;
+        }
+        if ($concat_accessory =~/0/){
+                print M $cl_num.$concat_accessory."\n";
+        }
+        print O "\n";
+        print U "\n";
+}
+close(F);
+close(O);
+close(U);
+close(M);